Kirk's Secret
by motleycruefan52
Summary: Admiral Marcus had given Jim a mission to capture & arrest John Harrison, Whom is a terrorist in the eyes of the federation. Will Jim find Harrison ? This is an Omegaverse Fan Fic. M/M


Jim was getting ready with the landing party that was going to go to Kronos' surface to arrest John Harrison. He started to get anxious about getting really close to Harrison without beating the living shit out of him.

Uhora was talking to the Klingons when Harrison suddenly showed up guns a blazing. Kirk & Spock ran out of their ship to help Uhora from being harmed and to capture Harrison. Bones is busy making sure the newbie's don't get killed on their first mission.

Jim beats the shit out of the Klingons and he didn't see the one that was behind him. Harrison shot the creature dead and dropped his weapon. "How many torpedoes are on your ship?!" demanded Harrison. "How Many!"

"Seventy-two." Said Jim flatly.

"I Surrender." Jim then proceeded to beat the shit out of him. He noticed that no bruises were appearing on Johns face.

"Captain!" said Uhora.

"Captain! He surrendered!" said Spock not at all impressed with his behavior.

Bones began to mutter under his breath. "God Dammit Jim! Your gonna hurt yourself!"

Kirk stopped beating on Harrison. His breathing is more labored and heavy from how exhausted he was beginning to feel.

"On behalf of Christopher Pike, my friend & father, I accept your surrender." Said Jim handcuffing Harrison and then walking back towards the trader ship they arrived on.

When they finally make back to the ship. Jim has Harrison escorted to the brig. As they are walking to the brig, Bones decides now is the time to fuss over Jim's vital signs & health status. He's surprised to notice that Jim's blood pressure is really low. But he notices also in the reading that he is heavily aroused. Bones demands that Jim & Harrison are to be escorted to the med bay to be looked over.

Jim has started to get more irritable as of recently. Bones can't help to wonder what Jim's second sex is but he refuses to do the test. But today Bones is making him do what HE wants him to do. For safety reasons only. Harrison quietly snickers to himself because he knows what Jim's second sex was as soon as he met him.

As Bones is taking Harrison's blood sample to test it, Jim suddenly snaps out of no where. "Man! You reek of straight up pheromones" he said as he's covering his nose with the crook of his elbow.

"Jesus Jim! Do you not know when to shut your trap?!Because your gonna be up shits creek if you keep up with that mouth of your! No wonder why your mom never stayed around cause it's filthy!" Bones said as he's telling Harrison to hold the gauze on the incision. "Jim! Go have a seat on that fuckin' bio-bed man!"

Jim does as he's told because he doesn't want Bones getting angrier than he already is. When Harrison was walking by all Jim could smell was his pheromones. His stomach began to turn from the pain it was starting to become excruciating when he came closer to his scent. Bones notices and he tells Jim to take a nap in his private sanctuary when he take breaks when he their blood samples to see what their status' are presented as.

When Harrison is finally locked away in the brig. He begins to relax a little knowing the his family is 'safe' for now. Knowing where they are being held currently at this time. Which also scares him because he doesn't know what Jim is like when provoked and he doesn't want to risk his families lives just to test how far he could go before he could break him into doing his bidding. He decides to rest his eyes waiting for Jim to come to him.

"Jim? Hey Jim? Wake up, I have something extremely important." Said Bones being as gentle as he could possibly get without touching Jim's skin. Not wanting to risk bonding with him accidently. Jim stretches & moans and faces Bones with a half groggy smile. "What Bones…" said Jim sleepily. He doesn't say anything until Jim sits up on the couch.

"What is it Bone? You look like you had just gotten your favorite cowboy boots pissed on." Said Jim trying to lighten up the mood. Bones laughs shaking his head at his ridiculous antics.

"Jim I really don't know how to say this without freaking you out…" he confesses knowing well that Jim is going to have a total bitch fit.

"Spill it Bones! This intensity is killing me!" said Jim trying not to be insincere.

"Jim…Man you are an omega. Now do not be pissed at me because I had noticed how Harrison was making you really uncomfortable. So here is your suppressants and your very own key to your personal heat room. Jim do not look at me like that. I swear if you cry you are gonna end looking like a alligator getting spanked by its mother on the fourth of July during rush hour!" said Bones really not in the mood for crocodile tears. "If you want to know more about omegas. Go speak to Shaura Holmes. She's an omega herself and she knows what it's like to go through what you are going through. Now go and see her in the omega sanctuary section of the ship. It's really close to the brigs. So no detours to visit Harrison. Am I clear!"

Jim decides to shower and change his clothing first before heading to the sanctuary to meet up with Shaura. His muscles had been getting achy and he has started to get serious cramps from what he can tell. He gets dressed and heads toward the brig. Spock tries to stop Jim but he tells him that he on a short medical leave instructed by Bones to not delay to where he needs to be and tells him that he has the bridge until he is feeling better. Spock nods and Jim continues towards his destination.

Shaura is in her office writing a report when Bones comms her to let her know that James Tiberius Kirk is on his way down to her due to his recent finding of his second sex's status. "Alright Bones thank you for letting me know ahead of time." She says as she goes to prepare her medical supplies that she needs to use to prep Jim for an ultrasound to make sure his ovaries & uterus are developing okay with no difficulties. After an hour later she hears a knock on the sanctuaries doors. "Come in Jim!" she says in a calm tone.

"Hello I'm Jim. I'm here to set up my…I don't know what… My sanctuary?" said Jim still confused is to what he should be doing. Shaura takes him to a dressing room and hands him a dressing gown.

"Okay Jim go and change into this gown and keep your underwear on. When your finished with that I want you to lay on this bio-bed okay." She said with a smile and heads out of the changing room. Jim begins to change his clothes and absorbs into his mind.

'Oh man! I can't believe that I'm an omega! I feel that I am not myself anymore! More frightened rather than brave! My ass is also itching something fierce! Dammit! Why couldn't I be an alpha or a fucking beta instead?! Now I have to find a mate to help me with my heats…this is going to be the end of me!'

Jim gets out of his thoughts when Shaura knocks on the door. "Are you alright Jim? Do you need help?" she asked being sincere. Jim unlocks the door and just lays down on the bio-bed.

"Okay Jim. I'm going to preform an ultrasound to make sure your body is developing properly. Are you feeling any discomfort or pain at this time?" she asked being completely serious.

"Um…if you mean the cramps and feeling really hot. No not yet. Knock on wood. Oh and is it weird if my butt is extremely, irritatingly so, right now. It's starting to annoy the shit out of me if I'm truthfully honest with you." Said Jim squirming at the thought of his ass being itchy.

"Yes those symptoms are completely normal for you to be feeling right now." She said as she's bringing over the ultrasound machine closer. "I'm going to need you to bring up the gown over your belly button Jim. This is going to be a little cold." She said as she squeezes out some of the blue gel onto his lower abdomen. "Now lets see…Hmm yes that looks good. Great! Everything is developed really well and your ovaries look like they are going to burst from how full they are!" Jim gives her a horrified look and she giggles. "Oh Jim! I didn't mean to freak you out by my comment I'm sorry." She said as she turns of the machine and gives him a damp paper towel to wipe away the gel. Jim lets out a sigh of relief and cleans his stomach.

"So am I able to leave yet?" he asked knowing possibly that the news might not be good.

"Oh Jim. Sense this is your first true heat, which just happens to sync with mine, you can't leave until it has passed. Which will be a total of three whole days. Do you know what a heat entails Jim?" she asked curiously.

Jim just looks at her as if she had shot at him with a stun gun. "No I have never experienced one before…what does it do?"

"Jim come and have a seat." She gestures towards the leather couch. "A omega heat consists of having a uncontrollable need to mate with an alpha. This sometimes happens to an omega when they have found their soulmate or an alphas scent triggers their heat early. Sense an alpha triggered your heat by just being in the room with him. It is more likely that you had been induced to have a early heat due to the alphas pheromones. When this does happen, the alpha that released their pheromones is normally the one to help thus said omega through their heat, but in your case you have the sanctuary med bay wing that I fought Star Flight to have them on each mission vessel they owned to ensure omega safety on each ship." She pauses to go get cups of tea Jim & Herself and then sits down again to continue. "Your body starts to develop the necessary organs to reproduce with the alpha to produce pups or kids in our case. During the sexual part of the heat. Your stamina will increase and you will be so horny that you would beg for a alphas cock to be inserted into your pleasure place. On the last day of your heat. At the height of your climax, the alpha will develop a thick ring of flesh at the base of his penis called a knot, right before you climax though he will make band bite at crook of your neck, then push in his final thrust into your pleasure place, the knot then begins to swell a little more bigger making sure that you & your alpha do not separate before your bond is complete. Which lasts about thirty minutes and the alphas knot deflates. At that time the heat over and you get one day to snuggle & cuddle your alpha until he or she feels its okay for you to be away from them."

"Is it possible to become pregnant during my first heat?" he asked quite seriously. She grabs his hand and pats it.

"Yes it is possible Jim. In the statistics that I had researched. One hundred percent of the time the newly bonded couple knows right away that they expecting immediately. The alpha normally is the first to notice the scent change of their omega."

"Okay. Shaura I'm kind of feeling tired. Could you please show me my room?" asked Jim yawning and places his hand over his mouth so he didn't feel rude.

Shaura just looks at him for a few minutes before nodding & smiling. She grabbed his hand and guided him to his room.

"Jim? If there is anything you need there is a blue button on your end table." She said as she was about to walk out of the room and then stops. "Oh and Jim if you need sexual stimulation. There are sex toys in the bottom dresser. They are not used yet. Good night." As soon as she left the room, he began to strip out of his clothes, and pulls out the lubricant & toys. Jim pleasured himself until he fell asleep.

Mean while in the brig. Bones is asking Harrison questions about his alpha status and if he was aware that he was going into a rut. Harrison growls with frustration that his omega had not come to him for help yet with his heat.

"Doctor how is the captain doing? He must smell delicious. The smell of his slick must have turned you on. Admit it you wanted to thrust into his sweet slick hole with all your might." Harrison laughs almost maliciously. Bones got tired of him trying to fuck with his mind and walked out. Spock was just walking in when he was leaving. He did not try to stop him. He gave Harrison a blank stare before interrogating him.

"Ah Commander Spock, it's so good to see you again. Tell has my omega asked for me yet? Hmm…I'm beginning to worry for him. Is he all right?"

Spock could see through the fake sentiment that he was trying to trick him in revealing information about the captain to him. He just scoffs at him. Harrison notices it and is not pleased with what he had heard. So he began to glare at Spock. He decided to pull a trick of his own against the prisoner.

"Sense you seem to be so concerned for my captains health & personal well being. Maybe I could see if he would not mind coming to see you. But it's up to him to decide. Not I but I must ask you to refrain from giving him unwanted advances. I will be here with his doctors as well to make sure he feels safe." Said Spock as Harrison is pacing back and forth in his glass prison. Spock turns away from the prisoner and smirks to himself.

Spock heads toward the sanctuary and comms Bones to meet him there. He hopes that Jim & Shaura do not mind going to amuse Harrison. Bones finally arrives and he tells him of his plan. He thinks he's fucking crazy but he doesn't care as long Jim & Shaura are safe from Harrison's clutches.

Spock knocks & rings the door. They wait a few minutes for one of them to answer and it's Shaura. She looks at them with smile. She leads to the living room to sit down while they waited for Jim to wake up. She goes to get the tea tray & biscuits.

"So what brings you two fine gentlemen to our door?" asked Shaura curious.

"Harrison wants to speak with Jim. He is very persistent in his demands. I do not wish to make either of you uncomfortable. I will understand if neither of you two want to go." Said Spock speaking with a firm voice.

Jim walks into the room only in his boxer shorts with nothing else on. Bones notices that Jim's abdomen had began to swell out a little. Showing that his heat had began. He smiles to his friend. He freezes noticing Bones & Spock in the room. He looks to Shaura in confusion. Shaura pats the cushion next to her. He sits down and grabs a cup of tea. He waits for one of them to speak.

Spock explains to Jim & Shaura his plan and what he was wondering if they would not mind doing so. Jim agrees that it would be a good idea. Plus he wants to know who Harrison actually is and why he surrendered so easily. Jim goes and gets dressed.

As they were walking to the brig, Jim gets the sudden feeling that he is doing what he had wanted sense he first smelt Harrison. His alpha. Jim suddenly stops in his tracks. 'My ALPHA! WHAT THE FUCK! MY HEAT IS GOING TO GET ME INTO SOME SERIOUS SHIT!' He continued on walking not to bring suspicion to his person so Spock, Bones, and Shaura wouldn't notice his unease. They enter the brig and the guard was giving Harrison his lunch. He noticed that the cells port hole was opened slightly. Harrison took a big inhale of the captains scent.

"Ah Captain it's so good to see you again. How are you feeling?"

Jim could not hide his sudden discomfort coming out of his anus. The slick was now pooling down his legs. Harrison's voice had done this much to his body. It's as if his body knows who his alpha is but his mind is like 'FUCK NO! DON'T YOU FUCKING DARE!' and he doesn't even realize that he is walking closer to the port hole. He doesn't even realize that he has began to shiver from being cold until Shaura puts a sweater onto his shoulders.

In a low voice she whispers for only him to hear. "Jim it's getting really hard for me to be in here around him. I'm going to go sit near the guard at the desk okay. Be careful."

Harrison smiles as he sees the only other omega other than his omega that is on the ship he's imprisoned on.

"Hello…"Jim says nervously.

"He speaks. Tell me Captain, How's your heat going so far? Do you feel that itch yet? Have you resorted to pleasure toys yet my treasure? Tell me I'm dying to know how you have handled your needs so I can give you absolute pleasure." Said Harrison speaking in a sultry voice. Jim hears a rumble or a growl coming from the cell as he sat down in front of the small bouncy ball sized open port hole.

"I…I need my alpha….everything hurts so badly. My stomach has began to swell out from how much pain I'm in. Look…" said Jim as he lifts up his t-shirt for Harrison to see his swollen red belly. Jim watches as Harrison opens his mouth and begins to pant from the beautiful display of submission from his omega.

"Oh Captain…" Harrison was cut off by Jim before he could continue.

"My name is Jim. If you would like to call me by my name." said Jim pulling his shirt back down over his belly with a wince. He sucks in a breathe from how painful the movement of putting his clothing back into place over his body.

"Jim. Your name is actually James. So James tell me what else you want me to do for you to ease your pain." Said Harrison.

"What is your full name?" asked Jim wondering what this alpha is hiding from him. Harrison sighs and kneels really close the port hole and gestures for Jim to get closer so he can hear him.

"My name is John Harrison and I'm a commander in Star Flights London division. But I was transferred to the San Francisco's division by Admiral Marcus. I have to admit to you that this is not my true identity though. My omega you are going to hear the truth from my lips before someone tells you lies about me. My actual name is Khan Noonien Singh. I am an augmented human being. I had been frozen for over three hundred plus years old. Marcus had found myself & my crew in my ship frozen in space floating into oblivion. He found me in my frozen prison. He woke me up and demanded me to create him a weapon of mass destruction. He took my family from me and held them hostage in order for me to do his bidding. The sector that he had created is called Sector fifty-one. When I had a chance to potentially save my family. I placed them into all those torpedoes in your weapons bay so that I could get them away from Sector fifty-one. I never told Marcus of my second sex status because he would have forced me to bond with his slut of a daughter. I took suppressants for betas to mask my sent until I got off of that god forsaken planet we call Earth. So please if would, call me Khan or Noonien. I'm sorry the information I had just given you was kept secret from you my treasure." Khan waited for Jim's response to his confession.

Spock steps forward to escort him away from the glass but is stopped by Bones' hand on his shoulder. Bones whispers to Spock.

"Let Jim decide for himself if he wants to mate with Singh or not Spock. After all it's his body." Said Bones release his shoulder and walking over to Shaura to check on her. They continued to look at Jim wondering what is going through his head.

Jim falls to his knees because he is in so much pain. He began to have tears falling down his face. Bones immediately rushes over to him to help him. Jim is on his back now on the floor whimpering in excruciating pain. Bones leans in to listen to what Jim is trying to tell him.

"Bones…I..I want to be… with my alpha…please it hurts too much…" Jim says as he goes unconscious. Bones picks up Jim and turns to look at Khan.

"You promise you will not try to escape or hurt James if we take you to his private sanctuary. He trusts you Khan and I don't want to find a body of my bed friend in his bed. Do you get what I'm saying? I am granting you immunity from punishment if you behave and not give us any problems while being escorted to his chambers. Is that understood?" said Bones almost on the verge of tears for his friend.

"I promise to all of you that I will not hurt my omega or any of the crew. But if anyone threatens to hurt James I will not be sorry for my actions." Khan said with a almost terrifyingly serious tone.

They place him shackles to walk in the hallway to Jim's chambers. Spock had his phaser drawn just incase Khan were to try to escape. Shaura opens the door to the sanctuary and Jim's room. Bones places James carefully down onto the bed. Bones leaves the room while Spock removes the shackles from Khan's wrists.

"If you hurt my Captain in anyway. I. WILL. END. YOU." Said Spock with a snarl. He closes the door and goes over to James.

"James, my sweet omega, we are finally alone at last. Wake up they are no longer going to disturb us my treasure." Said Khan looming over James. James opened his eyes to see his alphas piercing electric blue eyes looking down at him.

"Hello my Alpha." Jim said as he pulled Khan into a siring kiss.


End file.
